isCentroidedFromFile: Get mode from mzML data file

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Get mode from mzML data file

Description

The function extracts the mode (profile or centroided) from the raw mass spectrometry file by parsing the mzML file directly. If the object x stems from any other type of file, NAs are returned.

Usage

isCentroidedFromFile(x)

Arguments

x	An object of class OnDiskMSnExp.

Details

This function is much faster than isCentroided(), which estimates mode from the data, but is limited to data stemming from mzML files which are still available in their original location (and accessed with fileNames(x)).

Value

A named logical vector of the same length as x.

Author(s)

Laurent Gatto

Examples

library("msdata")
f <- proteomics(full.names = TRUE,
                pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
x <- readMSData(f, mode = "onDisk")
table(isCentroidedFromFile(x), msLevel(x))

lgatto/MSnbase documentation built on May 4, 2024, 5:55 p.m.